Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015871.1 Corchorus capsularis cultivar CVL-1 contig15892, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 6606
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33


Found at i:141 original size:13 final size:14

Alignment explanation


    Indices: 125--153  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

        115 ATAATCGGAT

                          
        125 TTTGCATCCAT-CA
          1 TTTGCATCCATGCA

                          
        138 TTTGCATCCATGCA
          1 TTTGCATCCATGCA

              
        152 TT
          1 TT

        154 AAATAGAAGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41


Consensus pattern (14 bp):   
TTTGCATCCATGCA

Found at i:4412 original size:21 final size:21

Alignment explanation


    Indices: 4356--4418  Score: 74
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       4346 ATGCTTGGAG

                                 
       4356 TAAGAATATTCCAATCGATTC
          1 TAAGAATATTCCAATCGATTC

               *  *  * *          
       4377 TATTG-CTACTACAATCGATTC
          1 TA-AGAATATTCCAATCGATTC

                                 
       4398 TAAGAATATTCCAATCGATTC
          1 TAAGAATATTCCAATCGATTC

       4419 CAAGTTTTGC


Statistics
Matches: 32,  Mismatches: 8, Indels: 4
        0.73            0.18        0.09

Matches are distributed among these distances:
  20    1  0.03
  21   30  0.94
  22    1  0.03

ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35


Consensus pattern (21 bp):   
TAAGAATATTCCAATCGATTC

Found at i:5162 original size:20 final size:21

Alignment explanation


    Indices: 5134--5172  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       5124 TTATAGCTAT

                *                
       5134 TTTTCTATAC-TTTTTACCAC
          1 TTTTATATACATTTTTACCAC

                               
       5154 TTTTATATACATTTTTACC
          1 TTTTATATACATTTTTACC

       5173 GTATTTTCTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    9  0.53
  21    8  0.47

ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56


Consensus pattern (21 bp):   
TTTTATATACATTTTTACCAC

Done.